User:Dong Woo Chin/Sandbox-HIF

Background
HIF (Hypoxia-inducible factor) is a necessary component for the regulation of oxygen in the human body. When a cell undergoes a state of hypoxia—low oxygen concentration—HIF starts a reaction chain in order to keep the cell from hypoxic damage, and allows it to recover back to normoxia. HIF-1 is a heterodimeric protein, composed of both an alpha (HIF-1α) and a beta subunit (HIF-1β) that interact and form the activated transcription factor during hypoxia. Under normal oxygen conditions HIF-1 is suppressed by many different regulating proteins, including prolyl hydroxylase-domain enzymes (PHDs) and the von Hippel-Lindau tumor suppressor protein (pVHL). These proteins stop HIF from being active and starting an unnecessary signal transduction pathway. Under the conditions where HIF -1 is unnecessary, PHD hydroxylates a certain amino acid within the HIF-1α subunit, and pVHL binds to the hydroxylated amino acid, which leads to the ubiquitation and proteosomal degradation of the HIF-1α subunit. Peet Lab from the University of Adelaide explains this pathway in detail.

Hydroxylation of Proline-564
In the presence of O2(Normoxia) and Iron, prolyl hydroxylase domain (PHD) enzymes are highly functional.Under normoxia, Pro564 of HIF-1α is hydroxylated to Hyp564 by PHD, which allows pVHL to bind the site.

Interaction between HIF-1α and pVHL
Hyp564 completes an elaborate network of hydrogen bonds, providing a chemical basis for efficient capture of HIF-1α after oxygen-dependent hydroxylation. The sites that are responsible for hydrogen bonding are N67, R69, L562, H2O, H115, S111, W117, and Hyp564. W88, Y98, S111, H115, and W117 make the shape of pocket shape of pocket which “complements precisely the up-pucker conformation of the hydroxyproline ring.” The binding of pVHL to hydroxylated HIF-α directs a multiprotein ubiqutin ligase to mediate proteosomal degradation of the HIF-1α subunit. Thus, the loss of HIF-1α prevents the activation of the transcription factor, HIF-1.

Bone Regeneration and HIF-1α
A 2007 experiment (Komatsu et al) explored HIF-1α’s involvement in bone regeneration. The experimenters differentiated utilized wild type HIF-1α+/+ and partially deficient HIF-1α+/-mice and compared femoral healing rates. The findings discovered that the HIF-1α partial deficiency enhances bone regeneration. However, promoted HIF-1α expression level by deletion of pVHL or by PHD inhibition improved bone regeneration and increased callus formation in mice. (Wan C et al, 2008 and Shen X et al, 2009) The conclusions from these studies are contrary to the findings of the previous study done by Komatsu et al.